Merge pull request #172 from GillesPy2/release_1_1_2

Release 1 1 2

.travis.yml

@@ -5,6 +5,7 @@ python: "3.6"
 install:
           - pip3 install .
           - pip3 install python-libsbml
+          - pip3 install cython
 script:
           python test/run_tests.py -m release
 

README.md

@@ -1,4 +1,4 @@
-# Gillespy2
+# GillesPy2
 
 
   GillesPy2 is a python library designed to create stochastic simulations for biochemical systems.  This package provides an object-oriented approach to creating mathematical models based on these real-world systems and simulates reaction events over time, selecting from a variety of algorithms including ODE solutions, the Gillespie Direct algorithm (SSA), and several variants of the SSA.  This library contains multiple versions of solvers to support a variety of user environments with optimized code for C++, Cython, and NumPy.  
@@ -7,6 +7,10 @@
 
 https://docs.google.com/forms/d/12tAH4f8CJ-3F-lK44Q9uQHFio_mGoK0oY829q5lD7i4/viewform
 
+![PyPI](https://img.shields.io/pypi/v/gillespy2.svg)
+![PyPI - License](https://img.shields.io/pypi/l/gillespy2.svg?color=green)
+![PyPI - Python Version](https://img.shields.io/pypi/pyversions/gillespy2.svg)
+
 
 ## Installation
 You can install gillespy2 through the following methods.
@@ -32,7 +36,7 @@ GillesPy2 performs stochastic biochemical simulations utilizing simplified objec
 2. call the model's '.run()' method.
 
 The run method can be customized using keyword arguments to select different solvers, random seed, data return type and more.
-For more detailed examples on how to use GillesPy2, please see the [Getting Started](/examples/Getting-Started.ipynb) notebook contained in the [examples](/examples) subdirectory.
+For more detailed examples on how to use GillesPy2, please see the [Getting Started](https://github.com/GillesPy2/GillesPy2/tree/master/examples/Getting-Started.ipynb) notebook contained in the [examples](https://github.com/GillesPy2/GillesPy2/tree/master/examples) subdirectory.
 
 ## Built With
 
@@ -42,7 +46,7 @@ For more detailed examples on how to use GillesPy2, please see the [Getting Star
 
 ## Contributing
 
-If you have any problems, or want to request a feature, please submit an issue to this repository.  If you want to contribute to GillesPy2, please follow the guidelines set forth in [CONTRIBUTING.md](CONTRIBUTING.md).  If you have any questions, contact Brian Drawert.
+If you have any problems, or want to request a feature, please submit an issue to this repository.  If you want to contribute to GillesPy2, please follow the guidelines set forth in [CONTRIBUTING.md](https://github.com/GillesPy2/GillesPy2/tree/master/CONTRIBUTING.md).  If you have any questions, contact Brian Drawert.
 
 ## Authors
 

docs/build/html/_modules/gillespy2/sbml/SBMLimport.html

@@ -86,8 +86,12 @@ <h1>Source code for gillespy2.sbml.SBMLimport</h1><div class="highlight"><pre>
             <span class="k">continue</span>
         <span class="n">name</span> <span class="o">=</span> <span class="n">species</span><span class="o">.</span><span class="n">getId</span><span class="p">()</span>
         <span class="k">if</span> <span class="n">species</span><span class="o">.</span><span class="n">isSetInitialAmount</span><span class="p">():</span>
-            <span class="n">value</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">species</span><span class="o">.</span><span class="n">getInitialAmount</span><span class="p">())</span>
-            <span class="n">mode</span> <span class="o">=</span> <span class="s1">&#39;dynamic&#39;</span>
+            <span class="n">int_value</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">species</span><span class="o">.</span><span class="n">getInitialAmount</span><span class="p">())</span>
+            <span class="n">value</span> <span class="o">=</span> <span class="n">species</span><span class="o">.</span><span class="n">getInitialAmount</span><span class="p">()</span>
+            <span class="k">if</span> <span class="n">value</span> <span class="o">==</span> <span class="n">int_value</span><span class="p">:</span>
+                <span class="n">value</span> <span class="o">=</span> <span class="n">int_value</span>
+                <span class="n">mode</span> <span class="o">=</span> <span class="s1">&#39;dynamic&#39;</span>
+            <span class="k">else</span><span class="p">:</span> <span class="n">mode</span> <span class="o">=</span> <span class="s1">&#39;continuous&#39;</span>
         <span class="k">elif</span> <span class="n">species</span><span class="o">.</span><span class="n">isSetInitialConcentration</span><span class="p">():</span>
             <span class="n">value</span> <span class="o">=</span> <span class="n">species</span><span class="o">.</span><span class="n">getInitialConcentration</span><span class="p">()</span>
             <span class="n">mode</span> <span class="o">=</span> <span class="s1">&#39;continuous&#39;</span>

docs/build/html/_modules/gillespy2/solvers/cpp/ssa_c_solver.html

@@ -77,8 +77,8 @@ <h1>Source code for gillespy2.solvers.cpp.ssa_c_solver</h1><div class="highlight
         <span class="n">outfile</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s2">&quot;};</span><span class="se">\n</span><span class="s2">unsigned int populations[] = {&quot;</span><span class="p">)</span>
         <span class="c1">#Write initial populations.</span>
         <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">species</span><span class="p">)</span><span class="o">-</span><span class="mi">1</span><span class="p">):</span>
-            <span class="n">outfile</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s1">&#39;</span><span class="si">{}</span><span class="s1">, &#39;</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">model</span><span class="o">.</span><span class="n">listOfSpecies</span><span class="p">[</span><span class="n">species</span><span class="p">[</span><span class="n">i</span><span class="p">]]</span><span class="o">.</span><span class="n">initial_value</span><span class="p">))</span>
-        <span class="n">outfile</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s1">&#39;</span><span class="si">{}</span><span class="s1">&#39;</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">model</span><span class="o">.</span><span class="n">listOfSpecies</span><span class="p">[</span><span class="n">species</span><span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">]]</span><span class="o">.</span><span class="n">initial_value</span><span class="p">))</span>
+            <span class="n">outfile</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s1">&#39;</span><span class="si">{}</span><span class="s1">, &#39;</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="nb">int</span><span class="p">(</span><span class="n">model</span><span class="o">.</span><span class="n">listOfSpecies</span><span class="p">[</span><span class="n">species</span><span class="p">[</span><span class="n">i</span><span class="p">]]</span><span class="o">.</span><span class="n">initial_value</span><span class="p">)))</span>
+        <span class="n">outfile</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s1">&#39;</span><span class="si">{}</span><span class="s1">&#39;</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="nb">int</span><span class="p">(</span><span class="n">model</span><span class="o">.</span><span class="n">listOfSpecies</span><span class="p">[</span><span class="n">species</span><span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">]]</span><span class="o">.</span><span class="n">initial_value</span><span class="p">)))</span>
         <span class="n">outfile</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s2">&quot;};</span><span class="se">\n</span><span class="s2">&quot;</span><span class="p">)</span>
     <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">reactions</span><span class="p">)</span> <span class="o">&gt;</span> <span class="mi">0</span><span class="p">:</span>
         <span class="c1">#Write reaction names</span>
@@ -204,7 +204,7 @@ <h1>Source code for gillespy2.solvers.cpp.ssa_c_solver</h1><div class="highlight
         <span class="k">if</span> <span class="n">built</span><span class="o">.</span><span class="n">returncode</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
             <span class="bp">self</span><span class="o">.</span><span class="n">compiled</span> <span class="o">=</span> <span class="kc">True</span>
         <span class="k">else</span><span class="p">:</span>
-            <span class="k">raise</span> <span class="n">gillespyError</span><span class="o">.</span><span class="n">BuildError</span><span class="p">(</span><span class="s2">&quot;Error encountered while compiling file:</span><span class="se">\n</span><span class="s2">Return code: </span><span class="si">{0}</span><span class="s2">.</span><span class="se">\n</span><span class="s2">Error:</span><span class="se">\n</span><span class="si">{1}</span><span class="se">\n</span><span class="s2">&quot;</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">built</span><span class="o">.</span><span class="n">returncode</span><span class="p">,</span> <span class="n">built</span><span class="o">.</span><span class="n">stderr</span><span class="p">))</span></div>
+            <span class="k">raise</span> <span class="n">gillespyError</span><span class="o">.</span><span class="n">BuildError</span><span class="p">(</span><span class="s2">&quot;Error encountered while compiling file:</span><span class="se">\n</span><span class="s2">Return code: </span><span class="si">{0}</span><span class="s2">.</span><span class="se">\n</span><span class="s2">Error:</span><span class="se">\n</span><span class="si">{1}</span><span class="se">\n</span><span class="si">{2}</span><span class="se">\n</span><span class="s2">&quot;</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">built</span><span class="o">.</span><span class="n">returncode</span><span class="p">,</span> <span class="n">built</span><span class="o">.</span><span class="n">stdout</span><span class="o">.</span><span class="n">decode</span><span class="p">(</span><span class="s1">&#39;utf-8&#39;</span><span class="p">),</span><span class="n">built</span><span class="o">.</span><span class="n">stderr</span><span class="o">.</span><span class="n">decode</span><span class="p">(</span><span class="s1">&#39;utf-8&#39;</span><span class="p">)))</span></div>
 
 <div class="viewcode-block" id="SSACSolver.run"><a class="viewcode-back" href="../../../../gillespy2.solvers.cpp.html#gillespy2.solvers.auto.ssa_solver.SSACSolver.run">[docs]</a>    <span class="k">def</span> <span class="nf">run</span><span class="p">(</span><span class="bp">self</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">model</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">t</span><span class="o">=</span><span class="mi">20</span><span class="p">,</span> <span class="n">number_of_trajectories</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span>
             <span class="n">increment</span><span class="o">=</span><span class="mf">0.05</span><span class="p">,</span> <span class="n">seed</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">debug</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span> <span class="n">profile</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span> <span class="n">show_labels</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
@@ -215,9 +215,18 @@ <h1>Source code for gillespy2.solvers.cpp.ssa_c_solver</h1><div class="highlight
             <span class="n">number_timesteps</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">t</span><span class="o">//</span><span class="n">increment</span> <span class="o">+</span> <span class="mi">1</span><span class="p">)</span>                    
             <span class="c1"># Execute simulation.</span>
             <span class="n">args</span> <span class="o">=</span> <span class="p">[</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">output_directory</span><span class="p">,</span> <span class="s1">&#39;UserSimulation&#39;</span><span class="p">),</span> <span class="s1">&#39;-trajectories&#39;</span><span class="p">,</span> <span class="nb">str</span><span class="p">(</span><span class="n">number_of_trajectories</span><span class="p">),</span> <span class="s1">&#39;-timesteps&#39;</span><span class="p">,</span> <span class="nb">str</span><span class="p">(</span><span class="n">number_timesteps</span><span class="p">),</span> <span class="s1">&#39;-end&#39;</span><span class="p">,</span> <span class="nb">str</span><span class="p">(</span><span class="n">t</span><span class="p">)]</span>
-            <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">seed</span><span class="p">,</span> <span class="nb">int</span><span class="p">):</span>
-                <span class="n">args</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="s1">&#39;-seed&#39;</span><span class="p">)</span>
-                <span class="n">args</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="nb">str</span><span class="p">(</span><span class="n">seed</span><span class="p">))</span>
+            <span class="k">if</span> <span class="n">seed</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
+                <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">seed</span><span class="p">,</span> <span class="nb">int</span><span class="p">):</span>
+                    <span class="n">args</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="s1">&#39;-seed&#39;</span><span class="p">)</span>
+                    <span class="n">args</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="nb">str</span><span class="p">(</span><span class="n">seed</span><span class="p">))</span>
+                <span class="k">else</span><span class="p">:</span>
+                    <span class="n">seed_int</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">seed</span><span class="p">)</span>
+                    <span class="k">if</span> <span class="n">seed_int</span> <span class="o">&gt;</span> <span class="mi">0</span><span class="p">:</span>
+                        <span class="n">args</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="s1">&#39;-seed&#39;</span><span class="p">)</span>
+                        <span class="n">args</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="nb">str</span><span class="p">(</span><span class="n">seed_int</span><span class="p">))</span>
+                    <span class="k">else</span><span class="p">:</span>
+                        <span class="k">raise</span> <span class="n">ModelError</span><span class="p">(</span><span class="s2">&quot;seed must be a positive integer&quot;</span><span class="p">)</span>
+
             <span class="n">simulation</span> <span class="o">=</span> <span class="n">subprocess</span><span class="o">.</span><span class="n">run</span><span class="p">(</span><span class="n">args</span><span class="p">,</span> <span class="n">stdout</span><span class="o">=</span><span class="n">subprocess</span><span class="o">.</span><span class="n">PIPE</span><span class="p">,</span> <span class="n">stderr</span><span class="o">=</span><span class="n">subprocess</span><span class="o">.</span><span class="n">PIPE</span><span class="p">)</span>
             <span class="c1"># Parse/return results.</span>
             <span class="k">if</span> <span class="n">simulation</span><span class="o">.</span><span class="n">returncode</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>